Good idea, but how to get it to catch on without publishing in Science? JPK
On Thu, May 31, 2012 at 4:21 PM, Dale Tronrud <[email protected]> wrote: > > On 05/31/12 12:07, Jacob Keller wrote: >> Alas, how many lines like the following from a recent Science paper >> (PMID: 22605777), probably reviewer-incited, could have been avoided! >> >> "Here, we present three high-resolution crystal structures of the >> Thermus thermophilus (Tth) 70S ribosome in complex withRMF, HPF, or >> YfiA that were refined by using data extending to 3.0 Å (I/sI = 1), >> 3.1 Å (I/sI = 1), and 2.75 Å (I/sI = 1) resolution, respectively. The >> resolutions at which I/sI = 2 are 3.2 Å, 3.4 Å, and 2.9 Å, >> respectively." >> > > I don't see how you can avoid something like this. With the new, > higher, resolution limits for data (which are good things) people will > tend to assume that a "2.6 A resolution model" will have roughly the > same quality as a "2.6 A resolution model" from five years ago when > the old criteria were used. K&K show that the weak high resolution > data contain useful information but certainly not as much information > as the data with stronger intensity. > > The resolution limit of the data set has been such an important > indicator of the quality of the resulting model (rightly or wrongly) > that it often is included in the title of the paper itself. Despite > the fact that we now want to include more, weak, data than before > we need to continue to have a quality indicator that readers can > use to assess the models they are reading about. While cumbersome, > one solution is to state what the resolution limit would have been > had the old criteria been used, as was done in the paper you quote. > This simply gives the reader a measure they can compare to their > previous experiences. > > Now would be a good time to break with tradition and institute > a new measure of quality of diffraction data sets. I believe several > have been proposed over the years, but have simply not caught on. > SFCHECK produces an "optical resolution". Could this be used in > the title of papers? I don't believe it is sensitive to the cutoff > resolution and it produces values that are consistent with what the > readers are used to. With this solution people could include whatever > noisy data they want and not be guilty of overstating the quality of > their model. > > Dale Tronrud > >> JPK >> >> >> >> On Thu, May 31, 2012 at 1:59 PM, Edward A. Berry <[email protected]> wrote: >>> Yes! I want a copy of this program RESCUT. >>> >>> REMARK 200 R SYM FOR SHELL (I) : 1.21700 >>> I noticed structure 3RKO reported Rmerge in the last shell greater >>> than 1, suggesting the police who were defending R-merge were fighting >>> a losing battle. And this provides a lot of ammunition to those >>> they are fighting. >>> >>> Jacob Keller wrote: >>>> >>>> Dear Crystallographers, >>>> >>>> in case you have not heard, it would appear that the Rmerge statistic >>>> has died as of the publication of PMID: 22628654. Ding Dong...? >>>> >>>> JPK >>>> >>>> -- >>>> ******************************************* >>>> Jacob Pearson Keller >>>> Northwestern University >>>> Medical Scientist Training Program >>>> email: [email protected] >>>> ******************************************* >>>> >>> >> >> >> >> -- >> ******************************************* >> Jacob Pearson Keller >> Northwestern University >> Medical Scientist Training Program >> email: [email protected] >> ******************************************* >> >> -- ******************************************* Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: [email protected] *******************************************
